shnitsel._generated_accessors¶

Classes¶

`DataArrayAccessor`
`DatasetAccessor`

Module Contents¶

class DataArrayAccessor(obj)¶

Bases: shnitsel._accessors.DAManualAccessor

_methods = ['norm', 'subtract_combinations', 'pairwise_dists_pca', 'sudi', 'hop_indices', 'relativize',...¶

norm(dim='direction', keep_attrs=None)¶

Wrapper for shnitsel.core.postprocess.norm().

Parameters:

dim (Hashable)
keep_attrs (bool | str | None)

Return type:

xarray.core.dataarray.DataArray

subtract_combinations(dim, labels=False)¶

Wrapper for shnitsel.core.postprocess.subtract_combinations().

Parameters:

dim (Hashable)
labels (bool)

Return type:

xarray.core.dataarray.DataArray

pairwise_dists_pca(**kwargs)¶

Wrapper for shnitsel.core.postprocess.pairwise_dists_pca().

Return type:: xarray.core.dataarray.DataArray

sudi()¶

Wrapper for shnitsel.core.postprocess.sudi().

Return type:: xarray.core.dataarray.DataArray

hop_indices()¶

Wrapper for shnitsel.core.postprocess.hop_indices().

Return type:: xarray.core.dataarray.DataArray

relativize(**sel)¶

Wrapper for shnitsel.core.postprocess.relativize().

Return type:: xarray.core.dataarray.DataArray

ts_to_time(delta_t=None, old='drop')¶

Wrapper for shnitsel.core.postprocess.ts_to_time().

Parameters:

delta_t (float | None)
old (Literal)

Return type:

xarray.core.dataset.Dataset | xarray.core.dataarray.DataArray

keep_norming(exclude=None)¶

Wrapper for shnitsel.core.postprocess.keep_norming().

Parameters:: exclude (Optional)
Return type:: xarray.core.dataarray.DataArray

calc_ci(confidence=0.95)¶

Wrapper for shnitsel.core.postprocess.calc_ci().

Parameters:: confidence (float)
Return type:: numpy.ndarray

time_grouped_ci(confidence=0.9)¶

Wrapper for shnitsel.core.postprocess.time_grouped_ci().

Parameters:: confidence (float)
Return type:: xarray.core.dataset.Dataset

to_xyz(comment='#')¶

Wrapper for shnitsel.core.postprocess.to_xyz().

Return type:: str

traj_to_xyz()¶

Wrapper for shnitsel.core.postprocess.traj_to_xyz().

Return type:: str

dihedral(i, j, k, l, deg=False, full=False)¶

Wrapper for shnitsel.core.postprocess.dihedral().

Parameters:

i (int)
j (int)
k (int)
l (int)
deg (bool)
full (bool)

Return type:

xarray.core.dataarray.DataArray

angle(i, j, k, deg=False)¶

Wrapper for shnitsel.core.postprocess.angle().

Parameters:

i (int)
j (int)
k (int)
deg (bool)

Return type:

xarray.core.dataarray.DataArray

distance(i, j)¶

Wrapper for shnitsel.core.postprocess.distance().

Parameters:

i (int)
j (int)

Return type:

xarray.core.dataarray.DataArray

trajs_with_hops()¶

Wrapper for shnitsel.core.postprocess.trajs_with_hops().

Return type:: list

get_hop_types()¶

Wrapper for shnitsel.core.postprocess.get_hop_types().

Return type:: dict

to_mol(charge=None, covFactor=1.2, to2D=True, molAtomMapNumber=None, atomNote=None, atomLabel=None)¶

Wrapper for shnitsel.core.postprocess.to_mol().

Return type:: rdkit.Chem.rdchem.Mol

default_mol()¶

Wrapper for shnitsel.core.postprocess.default_mol().

Return type:: rdkit.Chem.rdchem.Mol

convert_energy(to)¶

Wrapper for shnitsel.core.postprocess.convert_energy().

Parameters:: to (str)

convert_forces(to)¶

Wrapper for shnitsel.core.postprocess.convert_forces().

Parameters:: to (str)

convert_dipoles(to)¶

Wrapper for shnitsel.core.postprocess.convert_dipoles().

Parameters:: to (str)

convert_length(to)¶

Wrapper for shnitsel.core.postprocess.convert_length().

Parameters:: to (str)

flatten_levels(idx_name, levels, new_name=None, position=0, renamer=None)¶

Wrapper for shnitsel.core.xrhelpers.flatten_levels().

Parameters:

idx_name (str)
levels (Sequence[str])
new_name (str | None)
position (int)
renamer (Callable | None)

Return type:

xarray.Dataset | xarray.DataArray

expand_midx(midx_name, level_name, value)¶

Wrapper for shnitsel.core.xrhelpers.expand_midx().

Return type:: xarray.Dataset | xarray.DataArray

assign_levels(levels=None, **levels_kwargs)¶

Wrapper for shnitsel.core.xrhelpers.assign_levels().

Parameters:

levels (dict[str, numpy.typing.ArrayLike] | None)
levels_kwargs (numpy.typing.ArrayLike)

Return type:

xarray.Dataset | xarray.DataArray

mgroupby(levels)¶

Wrapper for shnitsel.core.xrhelpers.mgroupby().

Parameters:: levels (Sequence[str])
Return type:: xarray.core.groupby.DataArrayGroupBy | xarray.core.groupby.DatasetGroupBy

msel(**kwargs)¶

Wrapper for shnitsel.core.xrhelpers.msel().

Return type:: xarray.Dataset | xarray.DataArray

sel_trajs(trajids_or_mask, invert=False)¶

Wrapper for shnitsel.core.xrhelpers.sel_trajs().

Parameters:: trajids_or_mask (Sequence[int] | Sequence[bool])
Return type:: xarray.Dataset | xarray.DataArray

sel_trajids(trajids, invert=False)¶

Wrapper for shnitsel.core.xrhelpers.sel_trajids().

Parameters:: trajids (numpy.typing.ArrayLike)
Return type:: xarray.Dataset

smiles_map(charge=0, covFactor=1.5)¶

Wrapper for shnitsel.core.filter_unphysical.smiles_map().

Return type:: str

last_time_where()¶: Wrapper for shnitsel.core.filtre.last_time_where().

get_bond_lengths(bond_types=None, mol=None)¶: Wrapper for shnitsel.core.geom.get_bond_lengths().

get_bond_angles(angle_types=None, mol=None, deg=False)¶: Wrapper for shnitsel.core.geom.get_bond_angles().

get_bond_torsions(quadruple_types=None, mol=None, signed=False, deg=False)¶: Wrapper for shnitsel.core.geom.get_bond_torsions().

get_bats(mol=None, signed=False, deg=False)¶: Wrapper for shnitsel.core.geom.get_bats().

kabsch(reference_or_indexers=None, **indexers_kwargs)¶

Wrapper for shnitsel.core.geom.kabsch().

Parameters:: reference_or_indexers (xarray.core.dataarray.DataArray | dict | None)

FrameSelector(xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)¶: Wrapper for shnitsel.core.plot.select.FrameSelector().

TrajSelector(xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)¶: Wrapper for shnitsel.core.plot.select.TrajSelector().

frame3D()¶: Wrapper for shnitsel.core.plot.p3mhelpers.frame3D().

frames3Dgrid()¶: Wrapper for shnitsel.core.plot.p3mhelpers.frames3Dgrid().

traj3D()¶: Wrapper for shnitsel.core.plot.p3mhelpers.traj3D().

trajs3Dgrid(trajids=None, loop='forward')¶

Wrapper for shnitsel.core.plot.p3mhelpers.trajs3Dgrid().

Parameters:: trajids (list[int | str] | None)

pca(dim, n_components=2, return_pca_object=False)¶

Wrapper for shnitsel.core.ml.pca().

Parameters:

dim (str)
n_components (int)
return_pca_object (bool)

Return type:

tuple[xarray.core.dataarray.DataArray, sklearn.decomposition._pca.PCA] | xarray.core.dataarray.DataArray

lda(dim, cats, n_components=2)¶: Wrapper for shnitsel.core.ml.lda().

pls(yda, n_components=2, common_dim=None)¶: Wrapper for shnitsel.core.ml.pls().

class DatasetAccessor(obj)¶

Bases: shnitsel._accessors.DSManualAccessor

_methods = ['pca_and_hops', 'validate', 'ts_to_time', 'setup_frames', 'assign_fosc', 'broaden_gauss',...¶

pca_and_hops()¶

Wrapper for shnitsel.core.postprocess.pca_and_hops().

Return type:: tuple

validate()¶

Wrapper for shnitsel.core.postprocess.validate().

Return type:: numpy.ndarray

ts_to_time(delta_t=None, old='drop')¶

Wrapper for shnitsel.core.postprocess.ts_to_time().

Parameters:

delta_t (float | None)
old (Literal)

Return type:

xarray.core.dataset.Dataset | xarray.core.dataarray.DataArray

setup_frames(to_time=None, convert_to_eV=None, convert_e_kin_to_eV=None, relativize_energy=None, relativize_selector=None)¶

Wrapper for shnitsel.core.postprocess.setup_frames().

Parameters:

to_time (bool | None)
convert_to_eV (bool | None)
convert_e_kin_to_eV (bool | None)
relativize_energy (bool | None)

Return type:

xarray.core.dataset.Dataset

assign_fosc()¶

Wrapper for shnitsel.core.postprocess.assign_fosc().

Return type:: xarray.core.dataset.Dataset

broaden_gauss(fosc, agg_dim='frame', width=0.5, nsamples=1000, xmax=None)¶

Wrapper for shnitsel.core.postprocess.broaden_gauss().

Parameters:

fosc (xarray.core.dataarray.DataArray)
agg_dim (Hashable)
width (float)
nsamples (int)
xmax (float | None)

Return type:

xarray.core.dataarray.DataArray

get_per_state()¶

Wrapper for shnitsel.core.postprocess.get_per_state().

Return type:: xarray.core.dataset.Dataset

get_inter_state()¶

Wrapper for shnitsel.core.postprocess.get_inter_state().

Return type:: xarray.core.dataset.Dataset

calc_pops()¶

Wrapper for shnitsel.core.postprocess.calc_pops().

Return type:: xarray.core.dataarray.DataArray

find_hops()¶

Wrapper for shnitsel.core.postprocess.find_hops().

Return type:: xarray.core.dataset.Dataset

default_mol()¶

Wrapper for shnitsel.core.postprocess.default_mol().

Return type:: rdkit.Chem.rdchem.Mol

flatten_levels(idx_name, levels, new_name=None, position=0, renamer=None)¶

Wrapper for shnitsel.core.xrhelpers.flatten_levels().

Parameters:

idx_name (str)
levels (Sequence[str])
new_name (str | None)
position (int)
renamer (Callable | None)

Return type:

xarray.Dataset | xarray.DataArray

expand_midx(midx_name, level_name, value)¶

Wrapper for shnitsel.core.xrhelpers.expand_midx().

Return type:: xarray.Dataset | xarray.DataArray

assign_levels(levels=None, **levels_kwargs)¶

Wrapper for shnitsel.core.xrhelpers.assign_levels().

Parameters:

levels (dict[str, numpy.typing.ArrayLike] | None)
levels_kwargs (numpy.typing.ArrayLike)

Return type:

xarray.Dataset | xarray.DataArray

mgroupby(levels)¶

Wrapper for shnitsel.core.xrhelpers.mgroupby().

Parameters:: levels (Sequence[str])
Return type:: xarray.core.groupby.DataArrayGroupBy | xarray.core.groupby.DatasetGroupBy

msel(**kwargs)¶

Wrapper for shnitsel.core.xrhelpers.msel().

Return type:: xarray.Dataset | xarray.DataArray

save_frames(path, complevel=9)¶: Wrapper for shnitsel.core.xrhelpers.save_frames().

sel_trajs(trajids_or_mask, invert=False)¶

Wrapper for shnitsel.core.xrhelpers.sel_trajs().

Parameters:: trajids_or_mask (Sequence[int] | Sequence[bool])
Return type:: xarray.Dataset | xarray.DataArray

unstack_trajs()¶

Wrapper for shnitsel.core.xrhelpers.unstack_trajs().

Return type:: xarray.Dataset | xarray.DataArray

stack_trajs()¶

Wrapper for shnitsel.core.xrhelpers.stack_trajs().

Return type:: xarray.Dataset | xarray.DataArray

iconds_to_frames()¶: Wrapper for shnitsel.core.parse.sharc_icond.iconds_to_frames().

spectra_all_times()¶: Wrapper for shnitsel.core.plot.spectra3d.spectra_all_times().

energy_filtranda()¶

Wrapper for shnitsel.core.filtre.energy_filtranda().

Return type:: xarray.core.dataset.Dataset

get_cutoffs()¶: Wrapper for shnitsel.core.filtre.get_cutoffs().

truncate(cutoffs)¶: Wrapper for shnitsel.core.filtre.truncate().

write_ase(db_path, kind, keys=None, preprocess=True)¶

Wrapper for shnitsel.core.ase.write_ase().

Parameters:

db_path (str)
kind (str | None)
keys (Optional)
preprocess (bool)

pls_ds(xname, yname, n_components=2)¶: Wrapper for shnitsel.core.ml.pls_ds().